Cytoscape 2.x Plugins Release Note

Plugin Name: GeneMANIA

Version: 2.1

Release Note:

The GeneMANIA Cytoscape Plugin version 2.1 features the following changes:

New Features - Cytoscape:
* Users now have the option to download a specific data set from the website, instead of only the latest.
* Reworked network descriptions to provide more provenance and linkouts.
* Added "Attributes..." button on result page that allows users to
annotate their network's edges with information about the source networks those edges came from.
* Added more columns (PMID, publication details, etc.) to the network
table in flat file report (this used to all be clumped into the
"Description" column).
* Added more elements/attributes (PMID, publication details, etc.) to
the network section in the XML report.
* The query dialog now provides hints about what information the user still needs to provide.

New Features - Command Line Tools:
* Cross Validator and Network Assessor automatically detect whether a query has no negative examples. In such a case, automatic computation of negative examples is enabled (--auto-negatives).
* Query Runner's "genes" output format now sorts genes by score.

Bugs:
* Fixed a bug involving loading sessions that don't contain GeneMANIA metadata.
* Fixed numerous UI bugs in the query and import dialogs.
* Fixed issues with using the plugin and command line tools with data
sets that only contain custom organisms.
* Fixed an issue where new predictions can clobber the gene scores of
earlier predictions in the same Cytoscape session.

Command Line Tools:

The GeneMANIA plugin is distributed as a JAR file, which also contains a set of Java-based command line tools for performing predictions and managing data sets in an automatable way. Documentation for these tools can be found here:

http://www.genemania.org/plugin/tools.html

Compatibility:

This release works with Cytoscape 2.6.3+, 2.7, and 2.8. Sessions created by version 1.0 of the GeneMANIA plugin cannot be loaded fully by 2.1.